journal
MENU ▼
Read by QxMD icon Read
search

Journal of Bioinformatics and Computational Biology

journal
https://www.readbyqxmd.com/read/28918707/wdnfinder-a-method-for-minimum-driver-node-set-detection-and-analysis-in-directed-and-weighted-biological-network
#1
Chu Yanshuo, Wang Zhenxing, Wang Rongjie, Zhang Ningyi, Li Jie, Hu Yang, Teng Mingxiang, Wang Yadong
Structural controllability is the generalization of traditional controllability for dynamical systems. During the last decade, interesting biological discoveries have been inferred by applied structural controllability analysis to biological networks. However, false positive/negative information (i.e. nodes and edges) widely exists in biological networks that documented in public data sources, which can hinder accurate analysis of structural controllability. In this study, we propose WDNfinder, a comprehensive analysis package that provides structural controllability with consideration of node connection strength in biological networks...
September 4, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28893113/an-empirical-bayes-method-for-robust-variance-estimation-in-detecting-degs-using-microarray-data
#2
Na You, Xueqin Wang
The microarray technology is widely used to identify the differentially expressed genes due to its high throughput capability. The number of replicated microarray chips in each group is usually not abundant. It is an efficient way to borrow information across different genes to improve the parameter estimation which suffers from the limited sample size. In this paper, we use a hierarchical model to describe the dispersion of gene expression profiles and model the variance through the gene expression level via a link function...
August 25, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28877645/bone-marrow-cavity-segmentation-using-graph-cuts-with-wavelet-based-texture-feature
#3
Hironori Shigeta, Tomohiro Mashita, Junichi Kikuta, Shigeto Seno, Haruo Takemura, Masaru Ishii, Hideo Matsuda
Emerging bioimaging technologies enable us to capture various dynamic cellular activities in vivo. As large amounts of data are obtained these days and it is becoming unrealistic to manually process massive number of images, automatic analysis methods are required. One of the issues for automatic image segmentation is that image-taking conditions are variable. Thus, commonly, many manual inputs are required according to each image. In this paper, we propose a bone marrow cavity (BMC) segmentation method for bone images as BMC is considered to be related to the mechanism of bone remodeling, osteoporosis, and so on...
August 25, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28874087/systematic-investigations-of-gene-effects-on-both-topologies-and-supports-an-echinococcus-illustration
#4
Christophe Guyeux, Stéphane Chrétien, Nathalie M-L Côté, Jacques M Bahi
In this paper, we propose a high performance computing toolbox implementing efficient statistical methods for the study of phylogenies. This toolbox, which implements logit models and LASSO-type penalties, gives a way to better understand, measure, and compare the impact of each gene on a global phylogeny. As an application, we study the Echinococcus phylogeny, which is often considered as a particularly difficult example. Mitochondrial and nuclear genomes (19 coding sequences) of nine Echinococcus species are considered in order to investigate the molecular phylogeny of this genus...
August 16, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28874086/pacluster-clustering-polyadenylation-site-data-using-canonical-correlation-analysis
#5
Guoli Ji, Qianmin Lin, Yuqi Long, Congting Ye, Wenbin Ye, Xiaohui Wu
Alternative polyadenylation (APA) is a pervasive mechanism that contributes to gene regulation. Increasing sequenced poly(A) sites are placing new demands for the development of computational methods to investigate APA regulation. Cluster analysis is important to identify groups of co-expressed genes. However, clustering of poly(A) sites has not been extensively studied in APA, where most APA studies failed to consider the distribution, abundance, and variation of APA sites in each gene. Here we constructed a two-layer model based on canonical correlation analysis (CCA) to explore the underlying biological mechanisms in APA regulation...
August 16, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28718343/application-of-t-sne-to-human-genetic-data
#6
Wentian Li, Jane E Cerise, Yaning Yang, Henry Han
The t-distributed stochastic neighbor embedding t-SNE is a new dimension reduction and visualization technique for high-dimensional data. t-SNE is rarely applied to human genetic data, even though it is commonly used in other data-intensive biological fields, such as single-cell genomics. We explore the applicability of t-SNE to human genetic data and make these observations: (i) similar to previously used dimension reduction techniques such as principal component analysis (PCA), t-SNE is able to separate samples from different continents; (ii) unlike PCA, t-SNE is more robust with respect to the presence of outliers; (iii) t-SNE is able to display both continental and sub-continental patterns in a single plot...
June 23, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28659000/recurrent-neural-network-based-modeling-of-gene-regulatory-network-using-elephant-swarm-water-search-algorithm
#7
Sudip Mandal, Goutam Saha, Rajat Kumar Pal
Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. Inspired by the behavior of social elephants, we propose a new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN)...
June 13, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28610458/large-scale-parallel-genome-assembler-over-cloud-computing-environment
#8
Arghya Kusum Das, Praveen Kumar Koppa, Sayan Goswami, Richard Platania, Seung-Jong Park
The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research...
June 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28571482/introduction-to-selected-papers-from-the-8th-international-conference-on-bioinformatics-and-computational-biology-bicob-2016
#9
Nurit Haspel, Thomas Ioerger, Hisham Al-Mubaid
No abstract text is available yet for this article.
June 1, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28610459/an-automated-pipeline-for-mitochondrial-segmentation-on-atum-sem-stacks
#10
Weifu Li, Hao Deng, Qiang Rao, Qiwei Xie, Xi Chen, Hua Han
It is possible now to look more closely into mitochondrial physical structures due to the rapid development of electron microscope (EM). Mitochondrial physical structures play important roles in both cellular physiology and neuronal functions. Unfortunately, the segmentation of mitochondria from EM images has proven to be a difficult and challenging task, due to the presence of various subcellular structures, as well as image distortions in the sophisticated background. Although the current state-of-the-art algorithms have achieved some promising results, they have demonstrated poor performances on these mitochondria which are in close proximity to vesicles or various membranes...
May 26, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28571483/an-efficient-method-for-significant-motifs-discovery-from-multiple-dna-sequences
#11
Abdulrakeeb M Al-Ssulami, Aqil M Azmi, Hassan Mathkour
Identification of transcription factor binding sites or biological motifs is an important step in deciphering the mechanisms of gene regulation. It is a classic problem that has eluded a satisfactory and efficient solution. In this paper, we devise a three-phase algorithm to mine for biologically significant motifs. In the first phase, we generate all the possible string motifs, this phase is followed by a filtering process where we discard all motifs that do not meet the constraints. And in the final phase, motifs are scored and ranked using a combination of stochastic techniques and [Formula: see text]-value...
May 11, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28552033/microtarget-microrna-target-gene-prediction-approach-with-application-to-breast-cancer
#12
Hanaa Torkey, Lenwood S Heath, Mahmoud ElHefnawi
MicroRNAs are known to play an essential role in gene regulation in plants and animals. The standard method for understanding microRNA-gene interactions is randomized controlled perturbation experiments. These experiments are costly and time consuming. Therefore, use of computational methods is essential. Currently, several computational methods have been developed to discover microRNA target genes. However, these methods have limitations based on the features that are used for prediction. The commonly used features are complementarity to the seed region of the microRNA, site accessibility, and evolutionary conservation...
May 2, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28513252/a-novel-model-based-on-fcm-lm-algorithm-for-prediction-of-protein-folding-rate
#13
Longlong Liu, Mingjiao Ma, Jing Cui
The prediction of protein folding rates is of paramount importance in describing the protein folding mechanism, which has broad applications in fields such as enzyme engineering and protein engineering. Therefore, predicting protein folding rates using the first-order of protein sequence, secondary structure and amino acid properties has become a very active research topic in recent years. This paper presents a new fuzzy cognitive map (FCM) model based on deep learning neural networks which uses data obtained from biological experiments to predict the protein folding rate...
April 25, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28513253/synthesizing-large-scale-species-trees-using-the-strict-consensus-approach
#14
Jucheol Moon, Oliver Eulenstein
Supertree problems are a standard tool for synthesizing large-scale species trees from a given collection of gene trees under some problem-specific objective. Unfortunately, these problems are typically NP-hard, and often remain so when their instances are restricted to rooted gene trees sampled from the same species. While a class of restricted supertree problems has been effectively addressed by the parameterized strict consensus approach, in practice, most gene trees are unrooted and sampled from different species...
April 20, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28506097/a-computational-model-of-the-ca-2-transients-and-influence-of-buffering-in-guinea-pig-urinary-bladder-smooth-muscle-cells
#15
Vijay Dave, Rohit Manchanda
Many cellular events including electrical activity and muscle contraction are regulated and coordinated by intracellular [Formula: see text] concentration ([[Formula: see text]][Formula: see text]. In detrusor smooth muscle (DSM) cells, [[Formula: see text]]i is normally maintained at very low levels and rises transiently during signalling processes as a result of (i) influx from the extracellular space (mainly via L-type and T-type [Formula: see text] channels) and (ii) [Formula: see text] release from sarcoplasmic reticulum (SR) into the cytoplasm...
April 20, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28440122/effects-of-low-dose-ionizing-radiation-on-dna-damage-caused-pathways-by-reverse-phase-protein-array-and-bayesian-networks
#16
Dong-Chul Kim, Mingon Kang, Ashis Biswas, Chin-Rang Yang, Xiaoyu Wang, Jean X Gao
Ionizing radiation (IR) causing damages to Deoxyribonucleic acid (DNA) constitutes a broad range of base damage and double strand break, and thereby, it induces the operation of relevant signaling pathways such as DNA repair, cell cycle control, and cell apoptosis. The goal of this paper is to study how the exposure to low dose radiation affects the human body by observing the signaling pathway associated with Ataxia Telangiectasia mutated (ATM) using Reverse-Phase Protein Array (RPPA) and isogenic human Ataxia Telangiectasia (A-T) cells under different amounts and durations of IR exposure...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28274175/the-origins-and-evolutionary-history-of-human-non-coding-rna-regulatory-networks
#17
Masih Sherafatian, Seyed Javad Mowla
The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28052708/chaos-and-hyperchaos-in-simple-gene-network-with-negative-feedback-and-time-delays
#18
Tamara M Khlebodarova, Vladislav V Kogai, Stanislav I Fadeev, Vitaly A Likhoshvai
Today there are examples that prove the existence of chaotic dynamics at all levels of organization of living systems, except intracellular, although such a possibility has been theoretically predicted. The lack of experimental evidence of chaos generation at the intracellular level in vivo may indicate that during evolution the cell got rid of chaos. This work allows the hypothesis that one of the possible mechanisms for avoiding chaos in gene networks can be a negative evolutionary selection, which prevents fixation or realization of regulatory circuits, creating too mild, from the biological point of view, conditions for the emergence of chaos...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28033735/pass-based-approach-to-predict-hiv-1-reverse-transcriptase-resistance
#19
Olga Tarasova, Dmitry Filimonov, Vladimir Poroikov
HIV reverse transcriptase (RT) inhibitors targeting the early stages of virus-host interactions are of great interest to scientists. Acquired HIV RT resistance happens due to mutations in a particular region of the pol gene encoding the HIV RT amino acid sequence. We propose an application of the previously developed PASS algorithm for prediction of amino acid substitutions potentially involved in the resistance of HIV-1 based on open data. In our work, we used more than 3200 HIV-1 RT variants from the publicly available Stanford HIV RT and protease sequence database already tested for 10 anti-HIV drugs including both nucleoside and non-nucleoside RT inhibitors...
April 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27908222/contribution-of-bacterial-promoter-elements-to-transcription-start-site-detection-accuracy
#20
Milos Nikolic, Tamara Stankovic, Marko Djordjevic
Accurately detecting transcription start sites (TSS) is a starting point for understanding gene transcription, and an important ingredient in a number of applications necessary for functional gene annotation, such as gene and operon predictions. Available methods for TSS detection in bacteria use very different description of the bacterial promoter structure and all of them show low accuracy. It is therefore unclear which promoter features should be included in TSS recognition, and how their accuracy impacts the search detection...
April 2017: Journal of Bioinformatics and Computational Biology
journal
journal
40513
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"